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**Basic Usage of Trimmomatic**\\

The shell script below will trim/clean up Illumina paired reads (for options see http://www.usadellab.org/cms/?page=trimmomatic).\\ If you have your own set of adapters, lets say in the following path <ILLUMINACLIP:/path/to/userdir/Adapters.fas:2:30:10>, you need to place such information after you have declared the Paired and Unpaired file names. If you don't do this (because you don't know which adapters were used for the library), don't worry... you can use the script as it is, since trimmomatic will use its own Illumina provided adapters and search them (All adapters by default will be searched)\\  Do not forget to provide your directories names when __/path/to/userdir/__ appears

//input can be fastq (decompressed or compressed as gz), output will be decompressed by default.\\
always check if there is a newer update of Trimmomatic available in perun.//

== shell script: do no leave spaces between lines
<code>
#!/bin/bash
#$ -S /bin/sh
. /etc/profile
#$ -cwd
#$ -pe threaded 10
cd /path/to/userdir
java -jar /opt/perun/Trimmomatic-0.36/trimmomatic-0.36.jar PE -threads 10 -phred33 -trimlog LOG_NAME.out READS_R1.fastq READS_R2.fastq READS_R1_PairNtrim.fq READS_R1_unPairNtrim.fq READS_R2_PairNtrim.fq READS_R2_unPairNtrim.fq HEADCROP:20 LEADING:10 TRAILING:10 SLIDINGWINDOW:10:25 MINLEN:40
</code>

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